Modifying gather results to run for snps and indels.
Several changes
--Changed RCommandLineFunction to RscriptCommandLineFunction
----moved from using R CMD BATCH to Rscript
----removed extraneous parameters and added a args list parameter

--Adding nofp and nofn arguments to GatherResults.

--Adding cmdline parameter to make_graphs.r to specify output directory.
----Changed runAnalysis to pass an output directory name to make_graphs.R
Changing so that make_graphs is run twice, once for snps and once for indels.
--Altering GatherResults.scala so that it creates separate outputs for different variant types
----Passing file names as new parameters to make_graphs.r
Adding checks for missing files to make_graphs so that it doesn't crash if there are is no FN data.
Fixing missing parentheses.
Adding sep="" to all instances of the R paste function.
Merge branch 'gatherSnps'
GatherResults now draws graphs for SNPs and Indels when both data sets are available.
Conflicts:
	GatherResults.scala
Adding a minimum coverage parameter to SomaticSpike with a default of 5.
--This should hopefully screen out a lot of the garbage spike ins.
Adding a log notification each time a site is skipped due to low coverage.